Risk factors for viral RNA shedding in COVID-19 patients

Factors Associated with Prolonged SARS-CoV-2 Viral Positivity in an Italian Cohort of Hospitalized Patients

Clinical or microbiological factors potentially associated with prolonged COVID-19 PCR positivity are still poorly underexplored, but they could be of importance for public-health and clinical reasons. The objective of our analysis is to explore demographic, clinical, and microbiological factors potentially associated with a prolonged positivity to SARS-CoV-2 among 222 hospitalized patients. Prolonged detection positivity for SARS-CoV-2 RNA in swap samples, defined as positivity more than 21 days, was the outcome of interest. The 56 cases with a prolonged positivity to SARS-CoV-2 were matched for age and sex with 156 controls. The cases reported a significantly higher presence of diabetes mellitus, autoimmune diseases, chronic kidney diseases, and acute coronary syndrome. Moreover, the viral load was significantly higher in a period of prolonged positivity compared to a normal period. In the multivariable analysis, the presence of autoimmune diseases and chronic kidney disease were significantly associated with an increased risk of prolonged positivity as well as medium viral load or high viral load, i.e., low Ct value ≤ 30 indicating high viral load. The results of this study confirmed that in a large population of hospitalized patients with COVID-19 manifestations, the prolonged positivity of SARS-CoV-2 detection with nasopharyngeal swab was mainly related to autoimmune diseases, chronic kidney disease, and to baseline viral load.

Persistence of SARS-CoV-2 infection and viral intra- and inter-host evolution in COVID-19 hospitalized patients

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) persistence in COVID-19 patients could play a key role in the emergence of variants of concern. The rapid intra-host evolution of SARS-CoV-2 may result in an increased transmissibility, immune and therapeutic escape which could be a direct consequence of COVID-19 epidemic currents. In this context, a longitudinal retrospective study on eight consecutive COVID-19 patients with persistent SARS-CoV-2 infection, from January 2022 to March 2023, was conducted. To characterize the intra- and inter-host viral evolution, whole genome sequencing and phylogenetic analysis were performed on nasopharyngeal samples collected at different time points. Phylogenetic reconstruction revealed an accelerated SARS-CoV-2 intra-host evolution and emergence of antigenically divergent variants. The Bayesian inference and principal coordinate analysis analysis showed a host-based genomic structuring among antigenically divergent variants, that might reflect the positive effect of containment practices, within the critical hospital area. All longitudinal antigenically divergent isolates shared a wide range of amino acidic (aa) changes, particularly in the Spike (S) glycoprotein, that increased viral transmissibility (K417N, S477N, N501Y and Q498R), enhanced infectivity (R346T, S373P, R408S, T478K, Q498R, Y505H, D614G, H655Y, N679K and P681H), caused host immune escape (S371L, S375F, T376A, K417N, and K444T/R) and displayed partial or complete resistance to treatments (G339D, R346K/T, S371F/L, S375F, T376A, D405N, N440K, G446S, N460K, E484A, F486V, Q493R, G496S and Q498R). These results suggest that multiple novel variants which emerge in the patient during persistent infection, might spread to another individual and continue to evolve. A pro-active genomic surveillance of persistent SARS-CoV-2 infected patients is recommended to identify genetically divergent lineages before their diffusion.

A robust web-based tool to predict viral shedding in patients with Omicron SARS-CoV-2 variants

Background

Data on viral kinetics and variants affecting the duration of viral shedding were limited. Our objective was to determine viral shedding in distinct severe acute respiratory syndrome coronavirus 2 variants, including Omicron BA.4/5 and BF.7, and to identify the relevant influencing factors.

Methods

We carried out a longitudinal cohort study at Beijing Xiaotangshan Fangcang shelter hospital from May to June 2022 (Omicron BA.4/5) and from November to December 2022 (Omicron BF.7). Nucleocapsid protein (N) and open reading frame (ORF) genes were considered as the target genes of the reverse transcription PCR. The daily results of cycle threshold (CT), including lowest ORF1ab-CT values for days 1-3 post-hospitalisation and lowest N-CT values for days 1-3 post-hospitalisation (CT3minN) and demographic and clinical characteristics were collected.

Results

1433 patients with coronavirus disease 2019 (COVID-19) were recruited from the Fangcang shelter hospital, in which 278 patients were diagnosed with Omicron BA.4/5 and 1155 patients with Omicron BF.7. Patients with BF.7 infection showed a longer duration of viral shedding. The duration of viral shedding was associated with the variants age, alcohol use, the severity of COVID-19 and CT3minN. Moreover, the nomogram had excellent accuracy in predicting viral shedding.

Conclusions

Our results indicated that patients with Omicron BF.7 had a longer period of contagiousness than those with BA.4/5. The duration of viral shedding was affected by a variety of factors and the nomogram may become an applicable clinical instrument to predict viral shedding. Furthermore, we developed a new COVID-19 viral shedding predicting model that can accurately predict the duration of viral shedding for COVID-19, and created a user-friendly website to apply this prediction model (https://puh3.shinyapps.io/CVSP_Model/).

Analysis of the Factors That Affect the Detection Duration of SARS-CoV-2 in Loop Mediated Isothermal Amplification among COVID-19 Inpatients

In COVID-19 patients who are immunocompromised or have severe COVID-19, the duration of infectious viral shedding may be longer, and a longer isolation duration is recommended. At the National Sagamihara Hospital, a decline in the viral load to end the isolation of hospitalized patients with COVID-19 was confirmed using loop-mediated isothermal amplification (LAMP). However, a subset of patients displayed LAMP positivity for more than 20 days after symptom onset. Therefore, we conducted a retrospective observational study to investigate the factors that affect the persistence of LAMP positivity. This study included a total of 102 participants. The severity of COVID-19 was mild (25.5%), moderate (67.6%), or severe (6.9%). The median number (interquartile range) of days until negative LAMP results from symptom onset were 16 (14-19) days. Multivariate logistic regression analysis showed that patients ≥55 years and/or those with the delta variant were correlated with persistent LAMP positivity for more than 20 days after symptom onset. This study identified age, the delta variant, and oxygen requirement as factors that contribute to persistently positive LAMP results. Therefore, it is posited that in these patients, the implementation of LAMP for deisolation would result in a prolonged isolation duration.

The differences in virus shedding time between the Delta variant and original SARS-CoV-2 infected patients

Background

The worldwide epidemic of Coronavirus Disease 2019 (COVID-19) has evolved into multiple variants. The Delta variant is known for its ability to spread and replicate, while data are limited about the virus shedding time in patients infected by the Delta variant.

Methods

56 Delta variant and 56 original SARS-CoV-2 infected patients from Hunan, China, matched according to age and gender divided into two groups and compared the baseline characteristics and laboratory findings with appropriate statistical methods.

Results

Patients infected with the Delta variant had significantly fewer symptoms of fever (p < 0.001), fatigue (p = 0.004), anorexia (p < 0.001), shortness of breath (p = 0.004), diarrhea (p = 0.006), positive pneumonia rate of chest CT (p = 0.019) and chest CT ground glass opacities (p = 0.004) than those of patients with the original SARS-CoV-2. Patients of the Delta variant group had a significantly longer virus shedding time [41.5 (31.5, 46.75) vs. 18.5 (13, 25.75), p < 0.001] compared with the original SARS-CoV-2 group. The correlation analyses between the virus shedding time and clinical or laboratory parameters showed that the virus shedding time was positively related to the viral strain, serum creatinine and creatine kinase isoenzyme, while negatively correlated with lymphocyte count, total bilirubin and low-density lipoprotein. Finally, the viral strain and lymphocyte count were thought of as the independent risk factors of the virus shedding time demonstrated by multiple linear regression.

Conclusion

COVID-19 patients infected with the Delta variant exhibited fewer gastrointestinal symptoms and prolonged virus shedding time than those infected with the original SARS-CoV-2. Delta variant and fewer lymphocyte were correlated with prolonged virus shedding time.

Duration of SARS-CoV-2 RNA Shedding Is Significantly Influenced by Disease Severity, Bilateral Pulmonary Infiltrates, Antibiotic Treatment, and Diabetic Status: Consideration for Isolation Period

Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) ribonucleic acid (RNA) shedding is an important parameter for determining the optimal length of isolation period required for coronavirus disease 2019 (COVID-19) patients. However, the clinical (i.e., patient and disease) characteristics that could influence this parameter have yet to be determined. In this study, we aim to explore the potential associations between several clinical features and the duration of SARS-CoV-2 RNA shedding in patients hospitalized with COVID-19. A retrospective cohort study involving 162 patients hospitalized for COVID-19 in a tertiary referral teaching hospital in Indonesia was performed from June to December 2021. Patients were grouped based on the mean duration of viral shedding and were compared based on several clinical characteristics (e.g., age, sex, comorbidities, COVID-19 symptoms, severity, and therapies). Subsequently, clinical factors potentially associated with the duration of SARS-CoV-2 RNA shedding were further assessed using multivariate logistic regression analysis. As a result, the mean duration of SARS-CoV-2 RNA shedding was found to be 13 ± 8.44 days. In patients with diabetes mellitus (without chronic complications) or hypertension, the duration of viral shedding was significantly prolonged (≥13 days; p = 0.001 and p = 0.029, respectively). Furthermore, patients with dyspnea displayed viral shedding for longer durations (p = 0.011). The multivariate logistic regression analysis reveals that independent risk factors associated with the duration of SARS-CoV-2 RNA shedding include disease severity (adjusted odds ratio [aOR] = 2.94; 95% CI = 1.36-6.44), bilateral lung infiltrates (aOR = 2.79; 95% CI = 1.14-6.84), diabetes mellitus (aOR = 2.17; 95% CI = 1.02-4.63), and antibiotic treatment (aOR = 3.66; 95% CI = 1.74-7.71). In summary, several clinical factors are linked with the duration of SARS-CoV-2 RNA shedding. Disease severity is positively associated with the duration of viral shedding, while bilateral lung infiltrates, diabetes mellitus, and antibiotic treatment are negatively linked with the duration of viral shedding. Overall, our findings suggest the need to consider different isolation period estimations for specific clinical characteristics of patients with COVID-19 that affect the duration of SARS-CoV-2 RNA shedding.

Impact of antibody-level on viral shedding in B.1.617.2 (Delta) variant-infected patients analyzed using a joint model of longitudinal and time-to-event data

Knowledge of viral shedding remains limited. Repeated measurement data have been rarely used to explore the influencing factors. In this study, a joint model was developed to explore and validate the factors influencing the duration of viral shedding based on longitudinal data and survival data. We divided 361 patients infected with Delta variant hospitalized in Nanjing Second Hospital into two groups (≤ 21 days group and > 21 days group) according to the duration of viral shedding, and compared their baseline characteristics. Correlation analysis was performed to identify the factors influencing the duration of viral shedding. Further, a joint model was established based on longitudinal data and survival data, and the Markov chain Monte Carlo algorithm was used to explain the influencing factors. In correlation analysis, patients having received vaccination had a higher antibody level at admission than unvaccinated patients, and with the increase of antibody level, the duration of viral shedding shortened. The linear mixed-effects model showed the longitudinal variation of logSARS-COV-2 IgM sample/cutoff (S/CO) values, with a parameter estimate of 0.193 and a standard error of 0.017. Considering gender as an influencing factor, the parameter estimate of the Cox model and their standard error were 0.205 and 0.1093 (P = 0.608), the corresponding OR value was 1.228. The joint model output showed that SARS-COV-2 IgM (S/CO) level was strongly associated with the risk of a composite event at the 95% confidence level, and a doubling of SARS-COV-2 IgM (S/CO) level was associated with a 1.38-fold (95% CI: [1.16, 1.72]) increase in the risk of viral non-shedding. A higher antibody level in vaccinated patients, as well as the presence of IgM antibodies in serum, can accelerate shedding of the mutant virus. This study provides some evidence support for vaccine prevention and control of COVID-19 variants.

Plasma 25(OH)D Level is Associated with the Nucleic Acid Negative Conversion Time of COVID-19 Patients: An Exploratory Study

Purpose

Vitamin D, an essential nutrient and a pleiotropic steroid hormone, has been reported to be associated with the risk and severity in patients infected with Coronavirus Disease-2019 (COVID-19). The role of vitamin D in predicting clinical outcome for COVID-19 patients is unknown. Here, we aimed to determine the prognostic value of plasma 25(OH)D level in COVID-19 patients.

Patients and Methods

A total of 158 patients infected with novel COVID-19 Omicron variants in Shanghai were recruited in this study and were categorized into three groups by the tertile levels of plasma 25(OH)D. Plasma 25(OH)D level was determined along with routine blood tests related to liver and renal functions in newly diagnosed COVID-19 patients at admission. The nucleic acid negative conversion time of throat swab samples was evaluated as the primary clinical outcome. The prognostic value of clinical characteristics and plasma 25(OH)D level was assessed using the Kaplan-Meier plot and Cox proportional hazards regression tests.

Results

Higher level of plasma 25(OH)D level in COVID-19 patients was independently associated with shorter nucleic acid negative conversion time from COVID-19 infection (multivariate adjusted HR: 0.54, 95%CI: 0.35-0.82, P=0.004, tertile 2 vs 1; multivariate adjusted HR: 0.60, 95%CI: 0.39-0.90, P=0.014, tertile 3 vs 1).

Conclusion

Plasma 25(OH)D level may serve as an independent prognostic factor in COVID-19 patient. Our findings indicate the protective roles of vitamin D supplementation in the regiment of patients with COVID-19.

Association of underlying comorbidities and progression of COVID-19 infection amongst 2586 patients hospitalised in the National Capital Region of India: a retrospective cohort study

This study is conducted to observe the association of diabetes (DM), hypertension (HTN) and chronic kidney disease (CKD) on the prognosis and mortality of COVID-19 infection in hospital admitted patients with above mentioned comorbidities. This is a single centre, observational, retrospective study carried out at Sir Ganga Ram Hospital, Delhi, India. The burden of comorbidities on the prognosis and clinical outcome of COVID-19 patients admitted patients from April 8, 2020, to October 4, 2020. Chi-square and relative risk test were used to observe the association of comorbidities and disease prognosis. A total of 2586 patients were included in the study consisting of 69.6% of male patients. All the comorbidities were significantly associated with ICU admission and mortality. The relative risk showed that CKD is most prone to severity as well as mortality of the COVID-19 infection followed by HTN and DM. Further with the increase in number of underlying comorbidities, the risk of ICU admission and mortality also increases. Relative risk of the severity of COVID-19 infection in younger patients with underlying comorbidities are relatively at higher risk of severity of disease as well as to mortality compared to the elderly patients with similar underlying condition. Similarly, it is found that females are relatively at higher risk of mortality as compared to the males having same comorbid conditions except for the hypertensive patients. Diabetes, hypertension and CKD, all are associated with progression of COVID-19 disease to severity and higher mortality risk. The number of underlying comorbid condition is directly proportional to the progression of disease severity and mortality.

COVID-19 patient characteristics and time to viral clearance: A retrospective observational study in a multiethnic population (United Arab Emirates)

BACKGROUND

SARS-CoV-2 virus is the causing agent of COVID-19. The factors contributing to delayed viral clearance are still unclear.

METHODS

We investigated the factors influencing the time to viral clearance in COVID-19 patients using medical records from 1785 adult patients of various ethnicities treated at NMC Royal Hospital in Abu Dhabi, UAE. The Cox-proportional Hazard Model was utilized to identify risk variables for delayed viral clearance, and the Kaplan-Meier plot was used to measure the time to viral clearance among different groups.

RESULTS

several factors have been associated with an increased risk of delayed viral clearance, including advanced age (p = 0.006), presence of cardiovascular diseases (p = 0.016), presentation with upper respiratory tract infection (URTI) (p = 0.043), and combined gastrointestinal (GIT) and symptoms (URTI) (p = 0.012). ICU admission and severity of COVID-19 also increased the risk for delayed viral clearance (p = 0.006, p < 0.001, respectively). 'The overall median viral clearance time was 24 days. It was 32 days among patients over 60, 21 among those with URTI, GIT symptoms, and asymptomatic, 24 among diabetics, and 46.5 days among cardiovascular patients. The median time till viral clearance was 30 days among severe COVID-19 patients and 39 days among ICU-admitted patients.

CONCLUSIONS

We concluded that advanced age, cardiovascular comorbidities, disease presentation, and severe COVID-19 outcomes increased the risk of delayed viral clearance. Identifying these factors allow decision makers to implement an early and comprehensive management strategy to improve the outcome.

The efficacy of Zafirlukast as a SARS-CoV-2 helicase inhibitor in adult patients with moderate COVID-19 Pneumonia (pilot randomized clinical trial)

OBJECTIVE

To assess the efficacy of Zafirlukast as a SARS-CoV-2 Helicase Inhibitor in adult patients with moderate COVID-19 symptoms (hospitalized patients with COVID-19 pneumonia who were not admitted to an intensive care unit).

METHODS

We conducted a randomized, double blind, placebo-controlled, pilot trial with adult patients with moderate COVID-19 pneumonia. The sample was randomized to Zafirlukast 10 mg BD for 10 days plus standard care vs placebo plus standard care. The primary outcome was the complete resolution of all symptoms. The secondary outcomes were the duration of oxygen therapy, and length of hospital stay (LOS).

RESULTS

In total, 40 patients were randomized (20 to Zafirlukast and 20 to the control). The time to the resolution of clinical symptoms in both groups was not significantly different. Regarding the fever, 0.3 days [95 % CI, - 1.19, 0.69], p = 0.76, for shortness of breath, the difference was 0.4 days [95 % CI, - 2.67, 3.46], p = 0.68, for cough the difference was 0.2 days [95 % CI, - 1.45, 1.95], p = 0.98, for sputum the difference was 0.5 days [95 % CI, - 0.75, 1.85], p = 0.09, for vomiting the difference was 0.1 days [95 % CI, - 0.50, 0.30], p = 0.93, for fatigue the difference was 0.3 days [95 % CI, - 4.32, 3.62], p = 0.64. The LOS per day for the two groups was not significantly different, 1.1 days [95 % CI,- 2.03, 4.28], p = 0.94, nor was the duration of oxygen therapy per days, 1.3 days [95 % CI, - 1.79, 4.49], p = 0.49. Regarding the 7 category ordinary scale, there was no significant difference between the two groups at day 7 (p-value = 0.62), day 14 (p-value = 0.60) and day 28 (p-value = 0.48).

CONCLUSION

Among adult patients hospitalized with COVID-19 pneumonia, the treatment with Zafirlukast, compared to placebo, did not significantly improve symptoms resolution.

Association of symptom characteristics and comorbid conditions with viral RNA positivity of Covid-19 patients in Kasaragod district in Kerala, India: A retrospective cohort study

Background

Symptoms of Covid-19 are known to be non-specific ranging from asymptomatic cases to severe illness affecting multiple organ systems. The duration of viral RNA positivity and transmission varies in individuals. We describe the association between symptom characteristics and comorbid conditions with viral RNA positivity of SARSCoV-2 affected individuals.

Methods

We conducted a record-based retrospective cohort study of 179 patients found to be positive for Covid-19 in Kasaragod district in Kerala. We included details of all patients found positive during the initial phases of the pandemic and recorded details regarding symptoms, duration of viral RNA positivity and the occurrence of transmission. The data were analysed using SPSS.

Results

Any symptom was present in 68%. Fever (43%) was the most common symptom while 50% had at least one respiratory symptom. Increased duration of viral RNA positivity was found to be associated with presence of comorbid conditions. The majority of individuals who transmitted disease (75%) had some symptom, predominantly a respiratory symptom.

Conclusion

Respiratory symptoms are seen in half of the patients and viral RNA positivity was for a longer duration in patients with comorbid conditions.

Risk Factors for Slow Viral Decline in COVID-19 Patients during the 2022 Omicron Wave

Formulating termination of isolation (de-isolation) policies requires up-to-date knowledge about viral shedding dynamics. However, current de-isolation policies are largely based on viral load data obtained before the emergence of Omicron variant. In this retrospective cohort study involving adult patients hospitalised for COVID-19 between January and February 2022, we sought to determine SARS-CoV-2 viral shedding kinetics and to investigate the risk factors associated with slow viral decline during the 2022 Omicron wave. A total of 104 patients were included. The viral load was highest (Ct value was lowest) on days 1 post-symptom-onset (PSO) and gradually declined. Older age, hypertension, hyperlipidaemia and chronic kidney disease were associated with slow viral decline in the univariate analysis on both day 7 and day 10 PSO, while incomplete or no vaccination was associated with slow viral decline on day 7 PSO only. However, older age was the only risk factor that remained statistically significant in the multivariate analysis. In conclusion, older age is an independent risk factor associated with slow viral decline in this study conducted during the Omicron-dominant 2022 COVID-19 wave. Transmission-based precaution guidelines should take age into consideration when determining the timing of de-isolation.

SARS-CoV-2 Viral Shedding and Associated Factors among COVID-19 Inpatients and Outpatients

Background

According to the contagious ability of the new virus, SARS-CoV-2, characterization of viral shedding duration in the period of infection is highly valuable in terms of providing quarantine guidelines and isolation policies. Therefore, we aimed at viral shedding determination in 58 COVID-19 confirmed Iranian subjects in different stages.

Methods

58 COVID-19 confirmed Iranian subjects including 21 outpatients and 37 inpatients were investigated. The analytical data and clinical properties were documented in the standard questionnaire. The RT-PCR tests were done two and three weeks after the symptoms initiation.

Results

Viral eradication occurred in 44.8% two weeks after illness initiation whereas in 71% who achieved a negative PCR test in the third week. Moreover, prolonged viral shedding was observed in hospitalized cases in comparison to outpatients. Almost 30% of patients continued viral shedding three weeks after disease initiation.

Conclusion

A longer duration of viral shedding in hospitalized cases rather than outpatients was observed in this study. The results similar to other investigations call into question if the current policies are enough to prevent the viral spread or not. This study should be done on a larger sample to provide an appropriate time in isolation policy.

Drivers of adaptive evolution during chronic SARS-CoV-2 infections

In some immunocompromised patients with chronic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, considerable adaptive evolution occurs. Some substitutions found in chronic infections are lineage-defining mutations in variants of concern (VOCs), which has led to the hypothesis that VOCs emerged from chronic infections. In this study, we searched for drivers of VOC-like emergence by consolidating sequencing results from a set of 27 chronic infections. Most substitutions in this set reflected lineage-defining VOC mutations; however, a subset of mutations associated with successful global transmission was absent from chronic infections. We further tested the ability to associate antibody evasion mutations with patient-specific and virus-specific features and found that viral rebound is strongly correlated with the emergence of antibody evasion. We found evidence for dynamic polymorphic viral populations in most patients, suggesting that a compromised immune system selects for antibody evasion in particular niches in a patient’s body. We suggest that a tradeoff exists between antibody evasion and transmissibility and that extensive monitoring of chronic infections is necessary to further understanding of VOC emergence.

Analysis of mutations that arise in chronic SARS-CoV-2 infections shows both overlap and differences with mutations present in pandemic viral variants of concern, highlighting their distinct drivers of evolution.

Cytotoxic CD8-positive T-lymphocyte infiltration in the lungs as a histological pattern of SARS-CoV-2 pneumonitis

Despite millions of PCR confirmed cases of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection, the long-term pathophysiological changes induced by this infection in the lungs and their relationship with possible immune triggers remain incompletely understood. Acute respiratory distress syndrome and subsequent respiratory failure are the most common causes of mortality in hospitalised patients. Severe lung tissue destruction can be due to an overactive immune system that far exceeds the harm that would have been caused by direct virus replication. This study extends our previous investigation and presents detailed histopathological findings on cryotransbronchial biopsy in patients with persistent (range 31-182 days) pneumonitis and severe interstitial inflammatory infiltration in the lungs due to SARS-CoV-2 infection. We describe a novel lung injury pattern associated with SARS-CoV-2 pneumonitis, which manifests as a marked interstitial CD8-positive T-cell lymphocytic infiltration. These findings provide a better understanding of the changes in the lungs that ensue due to SARS-CoV-2 infection.

Duration of SARS-CoV-2 RNA positivity from various specimens and clinical characteristics in patients with COVID-19: a systematic review and meta-analysis

BACKGROUND

The duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA positivity will be important to prevent the spread of coronavirus disease 2019 (COVID-19). A systematic review and meta-analysis were conducted following PRISMA to determine the duration from several parts of the body and clinical characteristics affecting it.

MAIN TEXT

PubMed, Web of Science, Scopus, and CENTRAL were searched for original studies reporting the duration from COVID-19 onset to the disappearance of viral RNA. Of the 1682 studies identified, 100 met the selection criteria and 13,431 patients were included in this study. The duration of SARS-CoV-2 RNA positivity was 18.29 [95% confidence interval: 17.00-19.89] days in the upper respiratory tract samples, 23.79 [20.43-27.16] days in the sputum, 14.60 [12.16-17.05] days in the blood, and 22.38 [18.40-26.35] days in the stool. Sensitivity analysis revealed that the duration was positively correlated with age, comorbidities, severity, and usage of glucocorticoid. Subgroup analysis indicated that the presence or absence of complications had the greatest impact on the difference in DSRP.

CONCLUSIONS

The duration of SARS-CoV-2 RNA positivity was 18.29 days in the upper respiratory tract samples. The duration in the sputum and the stool was longer, while that in the blood was shorter. The duration in the upper respiratory tract samples was longer in older, with any comorbidities, severer, and treated with glucocorticoid. These results provide the basic data for the duration of SARS-CoV-2 RNA positivity, and in the future, the effect of vaccination against SARS-CoV-2 and the SARS-CoV-2 variants on the duration of RNA positivity should be assessed.

Predictors and time to recovery from COVID-19 among patients attended at the treatment centers in Ekiti State, South West, Nigeria

Introduction

time to clinical recovery from COVID-19 infection and associated factors has not been explored in Nigeria. This study was conducted to assess the predictors and time to recovery from COVID-19 among patients attended to at the treatment centers in Ekiti State, South West.

Methods

a facility-based retrospective cohort study was conducted between March 2020 to October 2021. Laboratory confirmed COVID-19 positive test result of 586 patients receiving treatment at the treatment centres in Ekiti were included. Data were extracted from COVID-19 intake forms and medical records of patients. Data were analysed using descriptive statistics and survival analysis methods including Cox proportional hazards regression model. Level of significance was set at 5%.

Results

the mean age of the patients was 43.46 (SD 0.74) years. Forty-seven percent (47%) of the patients were aged 25-44 years, fifty-one percent (51%) were males. The median recovery time of COVID-19 patients was 21 days (IQR: 14-23). Being a male-patient (95% CI 20.46-21.54), older age (95% CI 20.14-21.86), not admitted in the hospital (95% CI 22.74-23.26), and associated multiple co-morbidities (95% CI 17.65-28.35) were associated with delayed recovery time. Predictors of recovery time of patients from COVID-19 infection were admission status (aHR: 0.71, 95%CI 0.56-0.88; p=0.002) and symptoms on admission (aHR: 0.81, 95%CI 0.66-0.99; p=0.020).

Conclusion

patients with comorbidities, older and those not admitted were more likely to have a delayed clinical recovery from COVID-19. Knowledge of the predictors might help health professionals in risk stratification and better management of patients with COVID-19.

Estimate and determinants of SARS-CoV-2 RNA clearance time among non-severe COVID-19 patients

Objectives:

To estimate SARS-CoV-2 RNA clearance time among non-severe COVID-19 patients and explore factors associated with delayed negative conversion.

Methods:

A retrospective cohort study was conducted at the COVID-19 unit of a tertiary care center in the Western region of Saudi Arabia. Reverse transcriptase-polymerase chain reaction (RT-PCR) confirmed COVID-19 patients diagnosed between April 1 and June 30, 2020, were considered. The primary outcome was the time (days) from disease onset to first negative RT-PCR, which was analyzed using Kaplan–Meier and Cox regression survival methods. Demographic data, clinical history, baseline clinical, radiological and laboratory findings and management, and outcome data were collected and analyzed as factors associated with the viral RNA clearance time.

Results:

One hundred and forty-four patients were included. The mean (standard deviation [SD]) age was 36.93 (14.41) years, 50.7% were females, and 45.1% were healthcare workers. COVID19 was asymptomatic, mild and moderate in 11.1%, 71.5% and 17.4% of the participants, respectively. Fever (59.4%) and cough (58.0%) were the dominant onset symptoms. The mean viral RNA clearance time was 22.9 days (SD = 8.6; 95% confidence interval [CI] = 21.5–24.3 days). Extended clearance time was associated with older age (mean = 24.0 vs. 22.0 days; log-rank = 0.037), married status (23.2 vs. 22.6 days; log-rank = 0.021), working in health sector (24.2 vs. 21.8 days; log-rank = 0.006), and having a chronic disease (24.8 vs. 21.9 days; log-rank = 0.028), compared to their counterparts, respectively. In the adjusted model, the job sector was the only factor that was independently associated with clearance time. Non-healthcare sector showed hazard ratio 1.8 (95% CI = 1.3–2.7; log-rank = 0.002) with reference to healthcare sector.

Conclusion:

SARS-CoV-2 RNA clearance time is likely to be longer in non-severe COVID-19 patients, representing an additional risk for the virus dissemination among the community and calling for higher caution among the population.

Assessment of Factors Affecting Time to Recovery from COVID-19: A Retrospective Study in Ethiopia

Background. The average duration of recovery from COVID-19 and influencing factors, which would help inform optimal control strategies, remain unclear. Moreover, studies regarding this issue are limited in Ethiopia, and no region-wise studies were conducted. Hence, this study aimed to investigate the median recovery time from COVID-19, and its predictors among patients admitted to Amhara regional state COVID-19 treatment centers, Ethiopia. Methods. A facility-based retrospective follow-up study was conducted at Amhara regional state COVID-19 treatment centers from 13 March 2020 through 30 March 2021. Data were entered using EpiData version 3.1, and STATA version 14 was used for analysis. A Kaplan–Meier curve was used to estimate survival time, and the Cox regression model was fitted to identify independent predictors. $P$ value with 95% CI for the hazard ratio was used for testing the significance at alpha 0.05. Results. Six hundred twenty-two cases followed, and 540 observations developed an event at the end of the follow-up. The median time to recovery was 11 days with an interquartile range of 9–14 days. Most of the patients were recovered from COVID-19 between days seven and fourteen. In the first six days of admission, only 4.2% of cases had recovered, but by day 14, 73.8% had recovered. Patients without comorbid illness/s were faster to recover than their counterparts (AHR = 1.44 : 95% CI: 1.10, 1.91) and those who have signs and symptoms on admission (AHR = 0.42 : 95% CI: 0.30, 0.60) and old-aged (AHR = 0.988; 95% CI: 0.982, 0.994) took longer to recover. Conclusion. In conclusion, a relatively short median recovery time was found in this study. Significant predictors for delayed recovery from COVID-19 were older age, presence of symptoms at admission, and having at least one comorbid condition. These factors should be placed under consideration while developing a strategy for quarantining and treating COVID-19 patients.

Delayed Clearance of Viral RNA in Sputum for Severity COVID-19 Patients with Initial High Viral Load

Aim

To analyze the possible risk factors of delayed virus clearance in hospitalized patients with coronavirus disease 2019 (COVID-19).

Methods

Retrospective analysis of patients with COVID-19 admitted to the isolation wards from our hospital from 19th Jan 2020 to 18th March 2020. We were collected patient’s data including demographic, epidemiologic, and clinical information, as well as laboratory and radiologic findings. The possible confounding risk factors for prolonged viral RNA shedding of COVID-19 during hospitalization were explored by univariate analysis and any variables with a p value less than 0.05 after univariate analysis were included in a subsequent multivariate logistic regression model analysis.

Results

The 104 patients included 30 mild patients and 74 severe or critically ill patients. The median duration of viral RNA positivity in sputum was 11 days, and the longest duration of viral RNA positivity was 49 days after admission. Multivariate analysis shown that the used with darunavir/cobicistat treatment (odds ratio [OR]: 4.25, 95% confidence interval [CI]: 1.25–14.42, p = 0.020), duration of fever (OR: 1.15, 95% CI: 1.03–1.30, p = 0.015) and time to radiological improvement (OR: 1.14, 95% CI: 1.01–1.30, p = 0.033) were associated with delayed clearance of SARS-CoV-2 in sputum from COVID-19 patients. Then adjusted in the multivariate binary logistic regression analysis model in severe COVID-19 and found that critical COVID-19 patients (OR: 13.25, 95% CI: 1.45–12.07, p = 0.022), lower virus cycle threshold (CT) values of RT-PCR (OR: 0.96, 95% CI: 0.93–0.99, p = 0.004) and used with darunavir/cobicistat treatment (OR: 8.44, 95% CI: 2.21–32.28, p = 0.022) were associated with delayed clearance of SARS-CoV-2 in sputum from COVID-19 patients.

Conclude

Clearance of viral RNA in sputum was delayed in severe COVID-19 patients, especially with lower virus CT value. And antivirals with darunavir/cobicistat has little advantage in eliminating SARS-CoV-2.

The Persistence Time of SARS-CoV-2 RNA in hospitalized COVID-19 Patients: A prospective Study

BACKGROUND

In the late December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), the causative agent of coronavirus disease 2019 (COVID-19), spreads to almost all countries worldwide. The outbreak of this virus has also been confirmed since 19 February 2020 in Iran.

OBJECTIVE

The aim of this study was to investigate the time of viral RNA clearance in swab and serum samples of COVID-19 patients who received different medications. We also evaluated different factors that may be affected viral RNA persistence in patients infected by SARS-CoV-2.

METHODS

In March 2020, twenty-one hospitalized COVID-19 patients were participated in this prospective study. All patients received antiviral agents in their routine care. Throat swabs and blood samples were obtained from all patients in different intervals including day 3 or 5, day 7, day 10 and finally 14 days after the first positive real time RT-PCR (rRT-PCT) test Results: The median time from the SO to first negative rRT-PCR results for throat swabs and serum samples of COVID-19 patients were 18 and 14 days, respectively. These times were more significant in patients with lymphopenia, oxygen saturation ≤ 90% and comorbidity.

CONCLUSION

This preliminary study highlights that SASR-CoV-2 RNA was not detectable in the upper respiratory tract longer than three weeks. In addition, SARS-CoV may persist for a long period of time in the respiratory than the serum samples. This study support the idea that in the settings of limited resources the patients should cease to be tested earlier than three weeks for discharge management.

Risk factors for prolonged nucleic acid conversion time in patients with COVID-19

OBJECTIVES

The time for PCR positivity to negativity is defined as nucleic acid conversion time (NCT) and is very important in terminating the isolation of patients and determining infectiousness in patients with COVID-19. The aim of this study is to determine the median NCT and to evaluate the clinical and laboratory parameters affecting it in patients with COVID-19.

METHODS

This study included 318 patients with mild to moderate COVID-19 diagnosed with PCR positivity retrospectively.

RESULTS

The median NCT was 11 days. Patients were divided into 2 groups as early (<11 days) and late conversion (≥11 days). Older age, sore throat, onset fever, fever 72 h after hospitalization, history of exposure to SARS-CoV-2 virus without a mask, and moderated disease were significantly more common in the late conversion group. In addition, favipiravir use was higher in early conversion group and hydroxychloroquine use was higher in late conversion group. In multivariate analysis, sore throat (OR = 2.570; 95% CI: 1.051-6.284, P = 0.039) and hydroxychloroquine use (OR = 3.518, 95% CI: 1.163-10.635, P = 0,026) were independent risk factors for late conversion. Favipiravir use (OR = 0.062, 95% CI: 0.021-0.184, P = 0.0001) negatively affected the late conversion.

CONCLUSION

NCT was longer in patients with COVID-19 who had sore throat at admission and were treated with hydroxychloroquine instead of favipiravir.

Detection and predictors of anti-SARS-CoV-2 antibody levels in COVID-19 patients at 8 months after symptom onset

Aim: To determine SARS-CoV-2 specific IgM and IgG levels of patients with COVID-19 at 8 months after symptom onset and to explore the predictors of antibody levels. Materials & methods: The magnetic chemiluminescence method was used to measure the antibody levels. Clinical data were collected and analyzed retrospectively. Results: A total of 54 patients were enrolled in this study, of whom 59.3% were IgM positive and 96.4% were IgG positive. The multiple linear regression analysis revealed that the duration of RNA shedding, C-reactive protein level and disease severity were independent predictors of IgG levels. Conclusion: COVID-19 patients retained long-term viral-specific protective immunity. Disease severity, C-reactive protein level and duration of RNA shedding were related to antibody levels 8 months after symptom onset.

This study aimed to detect the levels of antibodies made by the body in response to COVID-19, 8 months after infection. We reviewed the characteristics of 54 patients with a history COVID-19 to find factors that may influence antibody levels. The results showed that 8 months after infection, almost all the patients had sufficient antibody levels to protect them from another episode of COVID-19 and that antibody levels were especially well maintained in those with a history of severe COVID-19.

Elevated Anti-SARS-CoV-2 Antibodies and IL-6, IL-8, MIP-1β, Early Predictors of Severe COVID-19

Viral and host immune kinetics during acute COVID-19 and after remission of acute symptoms need better characterization. SARS-CoV-2 RNA, anti-SARS-CoV-2 IgA, IgM, and IgG antibodies, and proinflammatory cytokines were measured in sequential samples from hospitalized COVID-19 patients during acute infection and six months following diagnosis. Twenty four laboratory confirmed COVID-19 patients with mild/moderate and severe COVID-19 were included. Most were males (83%) with a median age of 61 years. Twenty one percent were admitted to the intensive care unit (ICU) and eight of them (33.3%) met the criteria for severe COVID-19 disease. A delay in SARS-CoV-2 levels’ decline during the first six days of follow up, and viral load persistence until month 3 were related to severe COVID-19, but not viral load levels at the diagnosis. Higher levels of anti-SARS-CoV-2 IgA, IgM, IgG and the cytokines IL-6, IL-8 and MIP-1β at the diagnosis time were related to the severe COVID-19 outcome. Higher levels of MIP-1β, IL-1β, MIP-1α and IFN-γ were observed at month 1 and 3 during mild/moderate disease, compared to severe COVID-19. IgG persisted at low levels after six months of diagnosis. In conclusion, higher concentrations of IgA, IgM, and IgG, and IL-6, IL-8 and MIP-1β are identified as early predictors of COVID-19 severity, whereas no significant association is found between baseline SARS-COV-2 viral load and COVID-19 severity.

Median duration and factors that influence the duration of symptom resolution in COVID-19 patients in Ethiopia: A follow-up study involving symptomatic cases

Background

Understanding the clinical features of COVID-19 and duration for resolution of symptoms is crucial for isolation of patients and tailoring public health messaging, interventions and policy. Therefore, this study aims to assess the median duration of COVID-19 signs and symptoms' resolution and explore its predictors among symptomatic COVID-19 patients in Ethiopia.

Methods

A hospital-based prospective cohort study involving 124 COVID-19 cases was conducted at Eka Kotebe General Hospital, COVID-19 Isolation and Treatment Center. The study participants were all symptomatic COVID-19 adult patients admitted to the hospital from 18 March to 20 August 2020. Physicians at the centre recorded the data using a log sheet. Cox proportional-hazards regression model was conducted. Statistical significance was defined at P < 0.05.

Results

A total of 124 symptomatic COVID-19 patients with a mean age of 42 years (±17) were involved in the study. The median duration of symptom resolution of COVID-19 was seven days with a minimum of two and a maximum of sixty-eight days. Sex and body mass index (BMI) were statistically significant predictors of the symptom resolution. The hazard of having delayed sign or symptom resolution in males was 55% higher than in females (P = 0.039; CI: 0.22-0.96) and the hazard of delayed sign or symptom resolution in those with BMI ≥ 25 kg/m2 was 35% higher than in those with BMI < 25 kg/m2 (P = 0.041; CI: 0.44-0.98]).

Conclusions

The median duration of COVID-19 symptom resolution was seven days. Being male and/or having a BMI ≥ 25 kg/m2 were predictors of a delayed sign or symptom resolution time. Therefore, it is important to consider proportion of males and those with BMI ≥ 25 kg/m2 when preparing isolation and treatment centres. Males and individuals with BMI ≥ 25 kg/m2 shall also be given priority when shielding from the COVID-19.

Quantifying heterogeneity in SARS-CoV-2 transmission during the lockdown in India

The novel SARS-CoV-2 virus, as it manifested in India in April 2020, showed marked heterogeneity in its transmission. Here, we used data collected from contact tracing during the lockdown in response to the first wave of COVID-19 in Punjab, a major state in India, to quantify this heterogeneity, and to examine implications for transmission dynamics. We found evidence of heterogeneity acting at multiple levels: in the number of potentially infectious contacts per index case, and in the per-contact risk of infection. Incorporating these findings in simple mathematical models of disease transmission reveals that these heterogeneities act in combination to strongly influence transmission dynamics. Standard approaches, such as representing heterogeneity through secondary case distributions, could be biased by neglecting these underlying interactions between heterogeneities. We discuss implications for policy, and for more efficient contact tracing in resource-constrained settings such as India. Our results highlight how contact tracing, an important public health measure, can also provide important insights into epidemic spread and control.

Burns and COVID-19-Initial Experience and Challenges

The COVID-19 pandemic has brought with it many challenges in the field of healthcare around the world. Managing burn patients has its own challenges as they require a long duration of care and are more susceptible to infection. We conducted a retrospective observational study from January 30 to July 15, 2020 at our center to study the epidemiology of burns treated & patients and healthcare workers affected by COVID-19 during this period. The number of burn admissions showed a 42.6% reduction as compared to last year. A total of 17 patients (3.67%) and 29 health care workers (8.68%) tested positive for COVID-19 in the burns department. Our strategy underwent changes based on the changing dynamics of COVID-19 and changes in government and institutional policies. We have described the various challenges we faced in managing burns during this time. We found that effective screening of patients and healthcare workers, proper segregation of negative and positive/ suspect population and a low threshold for COVID-19 testing were essential to mitigate transmission of infection.

[SARS-CoV-2 and the digestive tract - Organoids to model gastrointestinal infection]

SARS-CoV-2 is a novel human pathogenic coronavirus whose predilection for the respiratory tract has given rise to a rapid pandemic spread via airborne particles. Organ-specific susceptibility is substantially determined by the density of cell surface expression of ACE2, which is exploited by viral spike protein as a receptor molecule to mediate adhesion and, thus, to permit internalization of the viral genome into the host cell. Based on an ample data set derived from clinical studies and case reports, evidence suggests that distinct cell populations of the digestive and olfactory-gustatory system are equally equipped with membrane-bound ACE2, rendering them "vulnerable" to SARS-CoV-2. Numerous reports on concomitant gastrointestinal complaints and laboratory abnormalities are thought to reflect a relevant degree of organ dysfunction and underscore the tropism of SARS-CoV-2 for the digestive tract. Organoids are three-dimensional in vitro replicas of organ tissue which, owing to their organotypic complex cellular composition and functional resemblance to primary cells, are particularly appreciated for basic research in the field of infectious diseases. This review specifically addresses the involvement of digestive organs by SARS-CoV-2 and outlines the significant contribution of organoid- and primary-cell culture-based models to gaining a deeper understanding of the underlying pathophysiological processes.

Detection and viral RNA shedding of SARS-CoV-2 in respiratory specimens relative to symptom onset among COVID-19 patients in Bavaria, Germany

We assessed severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) reverse transcriptase-polymerase chain reaction (RT-PCR) diagnostic sensitivity and cycle threshold (Ct) values relative to symptom onset in symptomatic coronavirus disease-2019 (COVID-19) patients from Bavaria, Germany, of whom a subset was repeatedly tested. Locally weighted scatterplot smoothing method was used to assess the relationship between symptom onset and Ct-values. Kaplan−Meier plots were used to visualise the empirical probability of detecting viral ribonucleic acid (RNA) over time and estimate the time until clearance of viral RNA among the repeatedly tested patients. Among 721 reported COVID-19 cases, the viral RNA was detected in specimens taken between three days before and up to 48 days after symptom onset. The mean Ct-value was 28.6 (95% confidence interval (CI) 28.2–29.0) with the lowest mean Ct-value (26.2) observed two days after symptom onset. Up to 7 days after symptom onset, the diagnostic sensitivity of the RT-PCR among repeatedly sampled patients (n = 208) remained above 90% and decreased to 50% at day 12 (95% CI 10.5–21.5). Our data provide valuable estimates to optimise the timing of sampling of individuals for SARS-CoV-2 detection. A considerable proportion of specimens sampled before symptom onset had Ct-values comparable with Ct-values after symptom onset, suggesting the probability of presymptomatic transmission.

Understanding viral shedding of severe acute respiratory coronavirus virus 2 (SARS-CoV-2): Review of current literature

OBJECTIVE

Transmission of SARS-CoV-2 has significant implications for hospital infection prevention and control, discharge management, and public health. We reviewed available literature to reach an evidenced-based consensus on the expected duration of viral shedding.

DESIGN

We queried 4 scholarly repositories and search engines for studies reporting SARS-CoV-2 viral shedding dynamics by PCR and/or culture available through September 8, 2020. We calculated the pooled median duration of viral RNA shedding from respiratory and fecal sources.

RESULTS

The review included 77 studies on SARS-CoV-2. All studies reported PCR-based testing and 12 also included viral culture data. Among 28 studies, the overall pooled median duration of RNA shedding from respiratory sources was 18.4 days (95% CI, 15.5-21.3; I2 = 98.87%; P < .01). When stratified by disease severity, the pooled median duration of viral RNA shedding from respiratory sources was 19.8 days (95% CI, 16.2-23.5; I2 = 96.42%; P < .01) among severely ill patients and 17.2 days (95% CI, 14.0-20.5; I2 = 95.64%; P < .01) in mild-to-moderate illness. Viral RNA was detected up to 92 days after symptom onset. Viable virus was isolated by culture from -6 to 20 days relative to symptom onset.

CONCLUSIONS

SARS-COV-2 RNA shedding can be prolonged, yet high heterogeneity exists. Detection of viral RNA may not correlate with infectivity since available viral culture data suggests shorter durations of shedding of viable virus. Additional data are needed to determine the duration of shedding of viable virus and the implications for risk of transmission.

Prolonged viral shedding and antibody persistence in patients with COVID-19

SARS-CoV-2 as a new global threat has affected global population for one year. Despite the great effort to eradicate this infection, there are still some challenges including different viral presentation, temporal immunity in infected individuals and variable data of viral shedding. We studied 255 COVID-19 suspected individuals to assess the viral shedding duration and also the antibody development against SARS-CoV-2 among the cases. Real Time RT-PCR assay was applied to determine the virus presence and SARS-CoV-2 antibodies were evaluated using SARS-CoV-2 IgM and IgG kits. 113 patients were confirmed for COVID-19 infection. The patients were followed until negative PCR achieved. The median viral shedding among studied population was obtained 34.16 (±17.65) days which was not significantly associated with age, sex and underlying diseases. Shiver and body pain were found in prolonged form of the infection and also patients who had gastrointestinal problems experienced longer viral shedding. Moreover, IgG was present in 84% of patients after 150 days. According to this data, the median viral shedding prolongation was 34.16 days which indicates that 14 days isolation might not be enough for population. In addition, IgG profiling indicated that it is persistent in a majority of patients for nearly 6 months which has brought some hopes in vaccine efficacy and application.

Laboratory correlates of SARS-CoV-2 seropositivity in a nationwide sample of patients on dialysis in the U.S

Patients on dialysis are at high risk for death due to COVID-19, yet a significant proportion do survive as evidenced by presence of SARS-CoV-2 antibodies in 8% of patients in the U.S. in July 2020. It is unclear whether patients with seropositivity represent the subgroup with robust health status, who would be more likely to mount a durable antibody response. Using data from a July 2020 sample of 28,503 patients receiving dialysis, we evaluated the cross-sectional association of SARS-CoV-2 seropositivity with laboratory surrogates of patient health. In separate logistic regression models, we assessed the association of SARS-CoV-2 seropositivity with seven laboratory-based covariates (albumin, creatinine, hemoglobin, sodium, potassium, phosphate, and parathyroid hormone), across the entire range of the laboratory and in comparison to a referent value. Models accounted for age, sex, region, race and ethnicity, and county-level COVID-19 deaths per 100,000. Odds of seropositivity for albumin 3 and 3.5 g/dL were 2.1 (95% CI 1.9-2.3) and 1.3 (1.2-1.4) respectively, compared with 4 g/dL. Odds of seropositivity for serum creatinine 5 and 8 mg/dL were 1.8 (1.6-2.0) and 1.3 (1.2-1.4) respectively, compared with 12.5 mg/dL. Lower values of hemoglobin, sodium, potassium, phosphate, and parathyroid hormone were associated with higher odds of seropositivity. Laboratory values associated with poorer health status and higher risk for mortality were also associated with higher likelihood of SARS-CoV-2 antibodies in patients receiving dialysis.

Comorbidities and Age Are Associated With Persistent COVID-19 PCR Positivity

Objectives

The impact of demographics and comorbidities on the duration of COVID-19 nasopharyngeal swab PCR positivity remains unclear. The objective of our analysis is to determine the impact of age, intensive care unit (ICU) admission, comorbidities, and ethnicity on the duration of COVID-19 PCR positivity among hospitalized patients in a large group of hospital.

Method

We studied 530 patients from a large hospital system and time to SARS-CoV-2 virus RNA PCR negativity at any-time during hospitalization or following discharge from the hospital was the primary endpoint. We included patients 18 years or older who tested positive for COVID-19 during an inpatient, outpatient, or emergency room visit between February 1, 2020, and April 14, 2020.

Results

Overall, 315 (59.4%) of our patient population continued to have a positive SARS-CoV-2 virus RNA PCR 4 weeks after the initial positive test. We found that age>70 years, chronic kidney disease, hypertension, hyperlipidemia, obesity, or coronary artery disease are associated with persistent PCR positivity for more than 4 weeks after initial diagnosis.

Conclusion

Age, and the presence of co-morbidities should be taken into consideration when interpreting a positive COVID PCR test.

Determining the communicable period of SARS-CoV-2: A rapid review of the literature, March to September 2020

IntroductionStandard testing for infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is based on RT-PCR tests, but detection of viral genetic material alone does not indicate ongoing infectious potential. The ability to isolate whole virus represents a better proxy for infectivity.AimThe objective of this study was to gain an understanding of the current literature and compare the reported periods of positive SARS-CoV-2 detection from studies that conducted RT-PCR testing in addition to experiments isolating whole virus.MethodsUsing a rapid review approach, studies reporting empirical data on the duration of positive RT-PCR results and/or successful viral isolation following SARS-CoV-2 infection in humans were identified through searches of peer-reviewed and pre-print health sciences literature. Articles were screened for relevance, then data were extracted, analysed, and synthesised.ResultsOf the 160 studies included for qualitative analysis, 84% (n = 135) investigated duration of positive RT-PCR tests only, 5% (n = 8) investigated duration of successful viral isolations, while 11% (n = 17) included measurements on both. There was significant heterogeneity in reported data. There was a prolonged time to viral clearance when deduced from RT-PCR tests compared with viral isolations (median: 26 vs 9 days).DiscussionFindings from this review support a minimum 10-day period of isolation but certain cases where virus was isolated after 10 days were identified. Given the extended time to viral clearance from RT-PCR tests, future research should ensure standard reporting of RT-PCR protocols and results to help inform testing policies aimed at clearance from isolation.

Clinical features in coronavirus disease 2019 (COVID-19) patients with early clearance and prolonged shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA

Background

Since the outbreak of coronavirus disease 2019 (COVID-19), the pattern of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA shedding has not been well characterized.

Methods

In our study, 652 patients in Wuhan Designated Hospital were recruited, and their clinical and laboratory findings were extracted and analyzed.

Results

The median duration of SARS-CoV-2 RNA detection was 23 days [interquartile range (IQR), 18 days] from symptom onset. Compared to patients with early viral RNA clearance (<23 days after illness onset), we found that patients with late viral RNA clearance (≥23 days) had a higher proportion of clinical features, as follows: symptoms, including fever, dry cough, and sputum production; comorbidities, including hypertension, chronic kidney disease, uremia, chronic liver disease, anemia, hyperlipidemia, and bilateral lung involvement; complications, such as liver injury; delayed admission to hospital; laboratory parameters at baseline, including higher eosinophils, uric acid, cholesterol, triglycerides, and lower hemoglobin; and less treatment with arbidol, chloroquine, or any antivirals. After generalized linear regression, prolonged SARS-CoV-2 RNA shedding was independently associated with younger age; delayed admission to hospital; symptoms including fever, shivering, and sputum production; comorbidities including hypertension, diabetes, cardiovascular disease, anemia, hyperlipidemia, uremia, and lung involvement; and higher alanine aminotransferase (ALT), uric acid, and cholesterol levels at baseline.

Conclusions

In conclusion, the factors mentioned above are associated with the negative conversion of SARS-CoV-2 RNA. A deeper insight into virological dynamics will be helpful for establishing patient discharge and quarantine release criteria.

Profiles of Peripheral Immune Cells of Uncomplicated COVID-19 Cases with Distinct Viral RNA Shedding Periods

The heterogeneity of immune response to COVID-19 has been reported to correlate with disease severity and prognosis. While so, how the immune response progress along the period of viral RNA-shedding (VRS), which determines the infectiousness of disease, is yet to be elucidated. We aim to exhaustively evaluate the peripheral immune cells to expose the interplay of the immune system in uncomplicated COVID-19 cases with different VRS periods and dynamic changes of the immune cell profile in the prolonged cases. We prospectively recruited four uncomplicated COVID-19 patients and four healthy controls (HCs) and evaluated the immune cell profile throughout the disease course. Peripheral blood mononuclear cells (PBMCs) were collected and submitted to a multi-panel flowcytometric assay. CD19⁺-B cells were upregulated, while CD4, CD8, and NK cells were downregulated in prolonged VRS patients. Additionally, the pro-inflammatory-Th1 population showed downregulation, followed by improvement along the disease course, while the immunoregulatory cells showed upregulation with subsequent decline. COVID-19 patients with longer VRS expressed an immune profile comparable to those with severe disease, although they remained clinically stable. Further studies of immune signature in a larger cohort are warranted.

Risk and predictive factors of prolonged viral RNA shedding in upper respiratory specimens in a large cohort of COVID-19 patients admitted to an Italian reference hospital

Background

Limited data are available about the predictors and outcomes associated with prolonged SARS-CoV-2 RNA shedding (VS).

Methods

A retrospective study including COVID-19 patients admitted to an Italian hospital between March 1 and July 1, 2020. Predictors of viral clearance (VC) and prolonged VS from the upper respiratory tract were assessed by Poisson regression and logistic regression analyses. The causal relation between VS and clinical outcomes was evaluated through an inverse probability weighted Cox model.

Results

The study included 536 subjects. The median duration of VS from symptoms onset was 18 days. The estimated 30-day probability of VC was 70.2%. Patients with comorbidities, lymphopenia at hospital admission, or moderate/severe respiratory disease had a lower chance of VC. The development of moderate/severe respiratory failure, delayed hospital admission after symptoms onset, baseline comorbidities, or D-dimer >1000 ng/mL at admission independently predicted prolonged VS. The achievement of VC doubled the chance of clinical recovery and reduced the probability of death/mechanical ventilation.

Conclusions

Respiratory disease severity, comorbidities, delayed hospital admission and inflammatory markers negatively predicted VC, which resulted to be associated with better clinical outcomes. These findings highlight the importance of prompt hospitalization of symptomatic patients, especially where signs of severity or comorbidities are present.

Understanding the outcomes of COVID-19 - does the current model of an acute respiratory infection really fit?

Although coronavirus disease 2019 (COVID-19) is regarded as an acute, resolving infection followed by the development of protective immunity, recent systematic literature review documents evidence for often highly prolonged shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in respiratory and faecal samples, periodic recurrence of PCR positivity in a substantial proportion of individuals and increasingly documented instances of reinfection associated with a lack of protective immunity. This pattern of infection is quite distinct from the acute/resolving nature of other human pathogenic respiratory viruses, such as influenza A virus and respiratory syncytial virus. Prolonged shedding of SARS-CoV-2 furthermore occurs irrespective of disease severity or development of virus-neutralizing antibodies. SARS-CoV-2 possesses an intensely structured RNA genome, an attribute shared with other human and veterinary coronaviruses and with other mammalian RNA viruses such as hepatitis C virus. These are capable of long-term persistence, possibly through poorly understood RNA structure-mediated effects on innate and adaptive host immune responses. The assumption that resolution of COVID-19 and the appearance of anti-SARS-CoV-2 IgG antibodies represents virus clearance and protection from reinfection, implicit for example in the susceptible-infected-recovered (SIR) model used for epidemic prediction, should be rigorously re-evaluated.

Factors Influencing Viral Clearance in Mild COVID-19 and Clinical Characteristics of Asymptomatic Patients

Background

The outbreak of coronavirus disease (COVID-19) has become a global public health emergency.

Objective

To evaluate the characteristics and outcomes of patients with COVID-19 in Anhui and to identify predictors of viral clearance.

Methods

We retrospectively analyzed the data collected from discharged patients with laboratory-confirmed SARS-CoV-2 infections. We compared clinical features between viral clearance and viral persistence, and evaluated factors associated with SARS-CoV-2 shedding using multiple linear regression.

Results

Among the 83 patients involved in the study, the median age was 43 years, while 60.2% were male, 35.4% had comorbidities, and the mortality was zero. The median time from illness onset to admission was 5 days (interquartile range (IQR), 2-7 days), and the median time from the illness onset to SARS-CoV-2 RNA detection was 16 days (IQR, 13-18 days). The factors influencing viral clearance were as follows: (1) delayed admission (beta 1.057, 95% CI 0.810-1.304; p ≤ 0.001) and (2) underlying comorbidities (beta 1.907, 95% CI 0.198-3.616; p = 0.029). No significant differences were observed in the length of stay (p = 0.246) and pneumonia between asymptomatic and symptomatic patients based on computed tomography (CT) (p = 0.124).

Conclusions

Delayed admission and underlying comorbidities may effectively predict SARS-CoV-2 RNA clearance. For those infected with SARS-CoV-2, even asymptomatic patients without any clinical symptoms should be traced and isolated. This practice may reduce the spread of SARS-CoV-2 and slow the COVID-19 pandemic caused by the virus. Clinical Trial Registration Number: This trial is registered with 2020-051.

Determinants of prolonged viral RNA shedding in hospitalized patients with SARS-CoV-2 infection

OBJECTIVE

To evaluate determinants of prolonged viral RNA shedding in hospitalized patients with SARS-CoV-2 infection.

MATERIALS AND METHODS

Hospitalized patients with SARS-CoV-2 positive nasopharyngeal RT-PCR were included in a single-center, retrospective study. Patients were divided in 2 groups according to the timing of viral clearance [≤14 days, "early clearance (EC)" and >14 days, "late clearance (LC)"].

RESULTS

179 patients were included in the study (101 EC, 78 LC), with median age 62 years. Median time of viral shedding was 14 days (EC/LC 10 and 19 days, respectively, P < 0.0001). Univariate analyses showed that age, male gender, receiving corticosteroids, receiving tocilizumab, ICU admission, low albumin and NLR ratio were associated with late viral clearance. In the multivariable analysis, older age (P = 0.016), albumin level (P = 0.048), corticosteroids (P = 0.021), and tocilizumab (P = 0.015) were significantly associated with late viral clearance.

CONCLUSIONS

Age, albumin, tocilizumab and corticosteroid treatment were independently associated with a prolonged SARS-CoV-2 RNA shedding.

Comparison of antiviral effect for mild-to-moderate COVID-19 cases between lopinavir/ritonavir versus hydroxychloroquine: A nationwide propensity score-matched cohort study

OBJECTIVES

We aimed to compare the antiviral effect of hydroxychloroquine (HCQ) and lopinavir/ritonavir (LPV/r) in patients with COVID-19.

METHODS

Nationwide retrospective case-control study was conducted to compare the effect of HCQ and LPV/r on viral shedding duration among patients with mild-to-moderate COVID-19 using the reimbursement data of National Health Insurance Service. After propensity score matching (PSM), multivariate analysis was conducted to determine statistically significant risk factors associated with prolonged viral shedding.

RESULTS

Overall, 4197 patients with mild-to-moderate COVID-19 were included. Patients were categorized into three groups: LPV/r (n = 1268), HCQ (n = 801), and standard care without HCQ or LPV/r (controls, n = 2128). The median viral shedding duration was 23 (IQR 17-32), 23 (IQR 16-32), and 18 (IQR 12-25) days in the LPV/r, HCQ, and control groups, respectively. Even after PSM, the viral shedding duration was not significantly different between LPV/r and HCQ groups: 23 (IQR, 17-32) days versus 23 (IQR, 16-32) days. On multivariate analysis, old age, malignancy, steroid use, and concomitant pneumonia were statistically significant risk factors for prolonged viral shedding.

CONCLUSION

The viral shedding duration was similar between HCQ and LPV/r treatment groups. There was no benefit in improving viral clearance compared to the control group.

SARS-CoV-2 associated COVID-19 in geriatric population: A brief narrative review

Coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has emerged as a fatal pandemic and has crushed even the world's best healthcare systems. Globally, it has affected 40,373,228 individuals and resulted in 1,119,568 deaths as of October 19, 2020. Research studies have demonstrated that geriatric population is vastly vulnerable to COVID-19 morbidity and mortality given their age and preexisting chronic comorbidities such as cardiovascular disease, hypertension, diabetes mellitus, chronic pulmonary and chronic kidney disease The data regarding susceptibility of elderly population to COVID-19 is accruing and suggests that factors like age, gender, chronic comorbidity, inflammaging, immunosenescence and renin angiotensin system may be the contributing risk factors towards COVID-19 and associated mortality in elderly population. Based on updated scientific literature, this narrative review précises the clinical presentations and underlying risk factors that might be associated with COVID-19 morbidity in geriatric population and provides informed insights, and discusses clinical presentation, psychosocial impact, mortality and potential corticosteroid treatment and prevention strategies of COVID-19 in older adults.

Risk factors associated with prolonged viral clearance in patients with a refractory course of COVID-19: a retrospective study

BACKGROUND

This study aimed to characterize a cohort of patients with a refractory course of COVID-19, and to investigate factors associated with the duration of viral clearance (DoVC).

MATERIALS & METHODS

A total of 65 patients with refractory COVID-19 were retrospectively enrolled from Huoshenshan Hospital. Univariate analysis and multivariate analysis were performed to examine the potential association between clinicopathologic characteristics and the DoVC.

RESULTS

The median DoVC in the overall study cohort was 48 days (ranged from 21 to 104 days). Multivariate analysis indicated that fever at illness onset (Hazard ratio (HR) = 4.897, 95% CI [1.809-13.260], p = 0.002), serum level of aspartate aminotransferase (AST) > 21.8 IU/L (HR = 3.010, 95% CI [1.195-7.578], p = 0.019), and titer of SARS-CoV-2 IgG > 142.09 AU/ml (HR = 3.061, 95% CI [1.263-7.415], p = 0.013) were the three independent risk factors associated with delayed viral clearance.

CONCLUSION

The current study suggested that clinical characteristics such as fever at illness onset, a high serum level of AST or SARS-CoV-2 IgG were associated with delayed viral clearance. Patients with these characteristics might need a more individualized treatment strategy to accelerate their recovery from the refractory COVID-19.

Time to recovery and its predictors among adults hospitalized with COVID-19: A prospective cohort study in Ethiopia

BACKGROUND

Various factors may determine the duration of viral shedding (the time from infection to viral RNA-negative conversion or recovery) in COVID-19 patients. Understanding the average duration of recovery and its predictors is crucial in formulating preventive measures and optimizing treatment options. Therefore, evidence showing the duration of recovery from COVID-19 in different contexts and settings is necessary for tailoring appropriate treatment and prevention measures. This study aimed to investigate the average duration and the predictors of recovery from Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection among COVID-19 patients.

METHOD

A hospital-based prospective cohort study was conducted at Eka Kotebe General Hospital, COVID-19 Isolation and Treatment Center from March 18 to June 27, 2020. The Center was the first hospital designated to manage COVID-19 cases in Ethiopia. The study participants were all COVID-19 adult patients who were admitted to the center during the study period. Follow up was done for the participants from the first date of diagnosis to the date of recovery (negative Real-time Reverse Transcriptase Polymerase Chain Reaction (rRT-PCT) test of throat swab).

RESULT

A total of 306 COVID-19 cases were followed up to observe the duration of viral clearance by rRT-PCR. Participants' mean age was 34 years (18-84 years) and 69% were male. The median duration of viral clearance from each participant's body was 19 days, but the range was wide: 2 to 71 days. Cough followed by headache was the leading sign of illness among the 67 symptomatic COVID-19 patients; and nearly half of those with comorbidities were known cancer and HIV/AIDS patients on clinical follow up. The median duration of recovery from COVID-19 was different for those with and without previous medical conditions or comorbidities. The rate of recovery from SARS-CoV-2 infection was 36% higher in males than in females (p = 0.043, CI: 1.01, 1.85). The rate of recovery was 93% higher in those with at least one comorbidity than in those without any comorbidity. The risk of delayed recovery was not influenced by blood type, BMI and presence of signs or symptoms. The findings showed that study participants without comorbidities recovered more quickly than those with at least one comorbidity. Therefore, isolation and treatment centers should be prepared to manage the delayed stay of patients having comorbidity.

Case Study: Prolonged Infectious SARS-CoV-2 Shedding from an Asymptomatic Immunocompromised Individual with Cancer

Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shedding was observed from the upper respiratory tract of a female immunocompromised individual with chronic lymphocytic leukemia and acquired hypogammaglobulinemia. Shedding of infectious SARS-CoV-2 was observed up to 70 days, and of genomic and subgenomic RNA up to 105 days, after initial diagnosis. The infection was not cleared after the first treatment with convalescent plasma, suggesting a limited effect on SARS-CoV-2 in the upper respiratory tract of this individual. Several weeks after a second convalescent plasma transfusion, SARS-CoV-2 RNA was no longer detected. We observed marked within-host genomic evolution of SARS-CoV-2 with continuous turnover of dominant viral variants. However, replication kinetics in Vero E6 cells and primary human alveolar epithelial tissues were not affected. Our data indicate that certain immunocompromised individuals may shed infectious virus longer than previously recognized. Detection of subgenomic RNA is recommended in persistently SARS-CoV-2-positive individuals as a proxy for shedding of infectious virus.

Diabetes mellitus is a risk factor for prolonged SARS-CoV-2 viral shedding in lower respiratory tract samples of critically ill patients

PURPOSE

The length of time a critically ill coronavirus disease 2019 (COVID-19) patient remains infectious and should therefore be isolated remains unknown. This prospective study was undertaken in critically ill patients to evaluate the reliability of single negative real-time polymerase chain reaction (RT-PCR) in lower tracheal aspirates (LTA) in predicting a second negative test and to analyze clinical factors potentially influencing the viral shedding.

METHODS

From April 9, 2020 onwards, intubated COVID-19 patients treated in the intensive care unit were systematically evaluated for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by RT-PCR of nasopharyngeal swabs and LTA. The time to negativity was defined as the time between the onset of symptoms and the viral clearance in LTA. In order to identify risk factors for prolonged viral shedding, we used univariate and multivariate Cox proportional hazards models.

RESULTS

Forty-eight intubated SARS-CoV-2 patients were enrolled. Overall, we observed that the association of the first negative RT-PCR with a second negative result was 96.7%. Median viral shedding was 25 (IQR: 21.5-28) days since symptoms' onset. In the univariate Cox model analysis, type 2 diabetes mellitus was associated with a prolonged viral RNA shedding (hazard ratio [HR]: 0.41, 95% CI: 0.06-3.11, p = 0.04). In the multivariate Cox model analysis, type 2 diabetes was associated with a prolonged viral RNA shedding (HR: 0.31, 95% CI: 0.11-0.89, p = 0.029).

CONCLUSION

Intubated patients with type 2 diabetes mellitus may have prolonged SARS-CoV-2 shedding. In critically ill COVID-19 patients, one negative LTA should be sufficient to assess and exclude infectivity.

Factors Associated with the Delayed Termination of Viral Shedding in COVID-19 Patients with Mild Severity in South Korea

Background and objectives: We aimed to analyze factors associated with the period of viral shedding in patients with confirmed COVID-19 who experienced only mild symptoms. Materials and methods: We conducted a multicenter retrospective study from three community treatment centers (CTCs) of South Korea. All patients included were admitted to the three centers before 31 March 2020. We collected data about clinical characteristics and the result of real-time reverse transcription polymerase chain reaction (RT-PCR). Results: Viral shedding was terminated within 32 days and 36 days in 75% and 90% of patients, respectively (range: 8–49 days). The mean period of viral shedding was 23.8 ± 8.7 days. In the multivariate Cox proportional hazards regression analysis, the existence of underlying comorbidities lowered the probability of the termination of viral shedding (HR = 0.561, 95% CI 0.388–0.812). Female sex and presence of COVID-19-associated symptoms also lowered the probability, but the significance was marginal. Conclusions: The existence of underlying comorbidities was associated with delayed termination of viral shedding in COVID-19 patients with mild severity.

Efficacy and safety of favipiravir, an oral RNA-dependent RNA polymerase inhibitor, in mild-to-moderate COVID-19: A randomized, comparative, open-label, multicenter, phase 3 clinical trial

Objective

To assess the efficacy and safety of favipiravir in adults with mild-to-moderate coronavirus disease 2019 (COVID-19).

Methods

In this randomized, open-label, parallel-arm, multicenter, phase 3 trial, adults (18–75 years) with RT-PCR confirmed COVID-19 and mild-to-moderate symptoms (including asymptomatic) were randomized 1:1 to oral favipiravir (day 1: 1800 mg BID and days 2−14: 800 mg BID) plus standard supportive care versus supportive care alone. The primary endpoint was time to the cessation of viral shedding; time to clinical cure was also measured.

Results

From May 14 to July 3, 2020, 150 patients were randomized to favipiravir (n = 75) or control (n = 75). Median time to the cessation of viral shedding was 5 days (95% CI: 4 days, 7 days) versus 7 days (95% CI: 5 days, 8 days), P = 0.129, and median time to clinical cure was 3 days (95% CI: 3 days, 4 days) versus 5 days (95% CI: 4 days, 6 days), P = 0.030, for favipiravir and control, respectively. Adverse events were observed in 36% of favipiravir and 8% of control patients. One control patient died due to worsening disease.

Conclusion

The lack of statistical significance on the primary endpoint was confounded by limitations of the RT-PCR assay. Significant improvement in time to clinical cure suggests favipiravir may be beneficial in mild-to-moderate COVID-19.